> Adding in any sort of extra meta data usually requires using YAML, the rules of which are a mystery to me.
That's not the fault of Markdown and not part of Markdown at all. Markdown doesn't say anything about metadata. Use of YAML at the top of Markdown documents was invented elsewhere (Jekyll, I believe), and any tools can use whatever they like.
> Numbered lists. Again, you need to use an editor to stay sane.
Or you can just type 1. in front of every line and let the Markdown renderer take care of numbering.
> What the hell are task lists anyways? Why do they exist?
Again, not a standard Markdown feature. They are a GitHub invention for adding checkboxes to issues and tracking the progress of things. They're convenient for places like GitHub, but if you're writing some documentation, you can just ignore them.
> The HTML output is antiquated at best. Though the basic structure of headers and paragraphs is generally semantic, there's no modern semantic elements such as main, article, section, nav, header, footer, figure, picture, etc.
YAGNI. And many of those would not necessarily be part of the Markdown document - in a blog, the would be outside of Markdown and instead part of the main template (which is by necessity HTMLish).
> Embedding videos, social media widgets, etc. isn't possible at all.
Why not? I can just copy-paste the embed widget from YouTube and paste it in my Markdown. The (Gruber) spec allows HTML inside Markdown. A thing that knows how to turn a link to the social-media-site-du-jour into a nice widget is outside the scope of a simple markup language (it would need a large database and constant updates).